2GMS

E coli GDP-4-keto-6-deoxy-D-mannose-3-dehydratase with bound hydrated PLP


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1MDOPDB entry 1MDO

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1629814% PEG 3400, 0.5 M MES buffer, 0.2 magnesium chloride, 0.1 M sodium chloride, 1 mM pyridoxal-5-phosphate, 2 mM 2-ketoglutarate, 1 mM GDP, Batch, pH 6.0, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.3447.41

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 74.9α = 90
b = 88.1β = 90
c = 125.8γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray277AREA DETECTORSIEMENS HI-STARsupper mirrors2005-10-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU2001.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.830920.05869.93.77661276612
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.81.88850.3231.41.58943

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 1MDO1.83071402714026249920.170.170.1620.213random
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
RMS Deviations
KeyRefinement Restraint Deviation
t_angle_deg1.9
t_bond_d0.008
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6260
Nucleic Acid Atoms
Solvent Atoms62
Heterogen Atoms35

Software

Software
Software NamePurpose
FRAMBOdata collection
XDSdata reduction
PHASERphasing
TNTrefinement
XDSdata scaling